> I used a vacuum equilibration and get the vlimit exceeded again in the
> first heating step.
You don't give the mdin for that run, so not able to comment.
> My solvated molecules simulations are still running
> the minimization step :
>
> minimization with restraint
> &cntrl
> imin=1,
> ntb=1,
> cut=10.0,
> maxcyc=10000, ncyc=1000,
> ntt=0, ntr=1,
> &end
> Hold the RNA fixed
> 1.0
> RES 1 343
> END
> END
>
> minimization solutes
> &cntrl
> imin=1,
> ntb=1,
> cut=10.0,
> maxcyc=10000, ncyc=1000,
> ntt=0,
> &end
>
My personal preference is to not bother with holding the solute
fixed because minimization is such a small move usually, but it
can't hurt.
ntb=1 here implies this mdin is for the solvated system, also
restraining the solute wouldn't make much sense for a vacuum
simulation (this could explain a blowup if it even ran with a
vacuum model):
> heat/dynamics at constant volume
> &cntrl
> imin=0,
> ntxo=1, ntrx=1,
> cut=10.0,tempi=0.1,
> ntpr=500, ntwx=500, ntwe=500,
> nstlim=100000, temp0=100.0,
> dt=0.0005,
> ntc=2, ntf=2, tol=0.00001,
> ntx=1, irest=0,
> ntb=1,tautp=1,
> ntt=1,
> nmropt=1,ntr=1
> /
> &wt
> type='TEMP0', istep1=0, istep2=40000, value1=0.1, value2=100.0,
> /
> &wt
> type='TEMP0', istep1=40001,istep2=100000,value1=100.0, value2=100.0,
> /
> &wt type='END',
> /
> GROUP FOR CONSTRAINTS
> 10.0
> RES 1 343
> END
> END
>
> The output files have
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.01 PRESS =
> 0.0
> Etot = -40689.5667 EKtot = 0.0998 EPtot =
> -40689.6665
> BOND = 54.3348 ANGLE = 1395.1889 DIHED =
> 281.6251
> 1-4 NB = 285.5361 1-4 EEL = 7286.8467 VDWAALS =
> 2993.9594
> EELEC = -52987.1576 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.8777E-04
> ------------------------------------------------------------------------------
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> ===============================================================================
> vlimit exceeded for step 6; vmax = 36.5222
> vlimit exceeded for step 7; vmax = 56.0527
> vlimit exceeded for step 8; vmax = 58.2767
> vlimit exceeded for step 9; vmax = 52.0658
> vlimit exceeded for step 10; vmax = 56.1929
>
>
> Thanks for your time
> Kirtana
> On Sun, Dec 4, 2011 at 11:10 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > > Dear Prof. Ross , if I understood correctly I make the changes for the
> > no
> > > shake ntc=1 ntf=1 (for the warming step and also for equilibration )
> > with
> > > time step dt=0.001
> >
> > I think with dt=1fs, ntc=2 is indicated.
> >
> > > and after heating I used ntx=5 with irest=1 .
> >
> > Correct.
> >
> > Bill
> >
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Received on Sun Dec 04 2011 - 21:30:02 PST
